title: Single-molecule FRET studies of counterion effects on the free energy landscape of human mitochondrial lysine tRNA.
abstract: The folding energy landscape of RNA is greatly affected by interactions between the RNA and counterions that neutralize the backbone negative charges and may also participate in tertiary contacts. Valence, size, coordination number, and electron shell structure can all contribute to the energetic stabilization of specific RNA conformations. Using single-molecule fluorescence resonance energy transfer (smFRET), we have examined the folding properties of the RNA transcript of human mitochondrial tRNA(Lys), which possesses two different folded states in addition to the unfolded one under conditions of thermodynamic equilibrium. We have quantitatively analyzed the degree of RNA tertiary structure stabilization for different types of cations based on a thermodynamic model that accounts for multiple conformational states and RNA-ion interactions within each state. We have observed that small monovalent ions stabilize the tRNA tertiary structure more efficiently than larger ones. More ions were found in close vicinity of compact RNA structures, independent of the type of ion. The largest conformation-dependent binding specificity of ions of the same charge was found for divalent ions, for which the ionic radii and coordination properties were responsible for shaping the folding free energy.
authors.affiliation: Institute of Biophysics, University of Ulm, 89069 Ulm, Germany.
authors.forename: Kirsten
authors.initials: K
authors.lastname: Dammertz
authors.forename: Martin
authors.initials: M
authors.lastname: Hengesbach
authors.forename: Mark
authors.initials: M
authors.lastname: Helm
authors.forename: G Ulrich
authors.initials: GU
authors.lastname: Nienhaus
authors.forename: Andrei Yu
authors.initials: AY
authors.lastname: Kobitski
mesh_terms: D002412:Cations / Q000378:metabolism / Q000494:pharmacology; D031541:Fluorescence Resonance Energy Transfer; D006801:Humans; D009690:Nucleic Acid Conformation / Q000187:drug effects; D012313:RNA / Q000737:chemistry* / Q000378:metabolism; D020871:RNA Stability / Q000187:drug effects; D012333:RNA, Messenger / Q000737:chemistry; D000077278:RNA, Mitochondrial; D012357:RNA, Transfer, Lys / Q000737:chemistry* / Q000378:metabolism; D013816:Thermodynamics
chemical_list: D002412:Cations; D012333:RNA, Messenger; D000077278:RNA, Mitochondrial; D012357:RNA, Transfer, Lys; D012313:RNA